Mercurial > repos > nml > mykrobe_parser
view test-data/prediction_2020/data/SRR3500411_MMUN.json @ 6:8e7e5a660942 draft
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
author | nml |
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date | Fri, 22 Sep 2023 17:24:02 +0000 |
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{ "SRR3500411_MMUN": { "susceptibility": { "Ofloxacin": { "predict": "S" }, "Moxifloxacin": { "predict": "S" }, "Isoniazid": { "predict": "S" }, "Kanamycin": { "predict": "S" }, "Ethambutol": { "predict": "S" }, "Streptomycin": { "predict": "S" }, "Ciprofloxacin": { "predict": "S" }, "Pyrazinamide": { "predict": "S" }, "Rifampicin": { "predict": "S" }, "Amikacin": { "predict": "S" }, "Capreomycin": { "predict": "S" } }, "phylogenetics": { "phylo_group": { "Mycobacterium_tuberculosis_complex": { "percent_coverage": 99.568, "median_depth": 114.0 } }, "sub_complex": { "Unknown": { "percent_coverage": -1, "median_depth": -1 } }, "species": { "Mycobacterium_africanum": { "percent_coverage": 62.167, "median_depth": 94.0 } }, "lineage": { "lineage": [ "clade_animal_A1" ], "calls_summary": { "clade_animal_A1": { "good_nodes": 1, "tree_depth": 1, "genotypes": { "clade_animal_A1": 1 } } }, "calls": { "clade_animal_A1": { "clade_animal_A1": { "G2873278T": { "variant": "ref-G2873278T?var_name=G2873278T&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=G2873278T", "genotype": [ 1, 1 ], "genotype_likelihoods": [ -11085.68809338619, -99999999, -274.747110554358 ], "info": { "coverage": { "reference": { "percent_coverage": 0.0, "median_depth": 0, "min_non_zero_depth": 0, "kmer_count": 0, "klen": 21 }, "alternate": { "percent_coverage": 100.0, "median_depth": 76, "min_non_zero_depth": 71, "kmer_count": 1518, "klen": 21 } }, "expected_depths": [ 114.0 ], "contamination_depths": [], "filter": [], "conf": 10811 }, "_cls": "Call.VariantCall" } } } } } }, "kmer": 21, "probe_sets": [ "tb-species-170421.fasta.gz", "tb-hunt-probe-set-jan-03-2019.fasta.gz", "tb.lineage.20200930.probes.fa.gz" ], "files": [ "SRR3500411_1.fastq", "SRR3500411_2.fastq" ], "version": { "mykrobe-predictor": "v0.10.0", "mykrobe-atlas": "v0.10.0" }, "genotype_model": "kmer_count" } }